GEMS Launcher Release Notes
September 2011: GEMS Launcher Release 5.5
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 8.4):
- Includes 43 new matrices (34 vertebrate, 9 plant).
- Library contains now 1326 matrices in 407 families.
- Updated Restriction Site Library (based on REBASE version
107).
- Extended Promoter Module Library (Module
Library Version 5.5):
April 2011: GEMS Launcher Release 5.4
- Option to upload user-defined models/matrices (binary files) from the Bioinformatics Workbench
- FrameWorker
- output limited to show at most 20 Java applets to avoid memory problems
- GeneRanker
- new classifiers based on Genomatix Literature Mining
- Diseases
- Tissues
- Co-cited genes
- Co-cited transcription factors
- improved algorithm for creation of gene-to-pathway-associations (Genomatix Signal Transduction
Pathways)
December 2010: GEMS Launcher Release 5.3
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 8.3):
- Includes 117 new matrices (106 vertebrate, 8 plant, 3 insect).
- Library contains now 1283 matrices in 398 families.
- Updated Restriction Site Library (based on REBASE version
010).
- Extended Promoter Module Library (Module
Library Version 5.4):
August 2010: GEMS Launcher Release 5.2.2
- New Genomatix look & feel
- Projects (including all results & data) can now be archived and
downloaded as a compressed file (see
project management)
- MatDefine:
- Enhanced motif definition for binding sequences where the orientation of the binding site is unknown.
- Allows selection of matrix library groups with which the new matrix should be compared.
- MatInspector: improved p-value calculation for common TF binding sites.
- Re-designed, clearly arranged main menu consistent with the newly introduced navigation bar.
- FrameWorker: supports selection of mandatory sequences that must contain the frameworks.
- CoreSearch: The random expectation value (RE-value) of the defined motifs is given in the ouput in order to estimate the quality of the motifs.
- ModelInspector: Per default, only non-redundant matches shown in the match overview are displayed in the "detailed output". Alternative, overlapping model matches can be added optionally.
February 2010: GEMS Launcher Release 5.2
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 8.2):
- Includes 60 new matrices (10 vertebrate, 7 plant, 43 insect).
- Library contains now 1166 matrices in 386 families.
- Updated Restriction Site Library (based on REBASE version
001).
- Extended Promoter Module Library (Module
Library Version 5.3):
- FastM: selection of matrix library version is supported (by default the latest matrix library version is used).
December 2009: GEMS Launcher Release 5.1.1
- GeneRanker:
- Allows new identifier types as input (Accession Numbers, Gene Names/Symbols, Affymetrix Probe Set IDs).
- Allows to use an example input set.
- When using "Signal Transduction Pathways (canonical)" as annotation type, the user can go directly to
the corresponding pathways in Genomatix Pathway System.
All canonical pathways are derived from Homo sapiens. If genes from other organisms are entered, these genes are mapped via orthology to their corresponding genes in Homo sapiens, if possible.
- FrameWorker now accepts up to 1000 input sequences.
- CoreSearch ("large scale" version):
- Enhanced comparison of motifs defined from subsets.
- Similarity of motifs defined from subsets is given in the output in order to assess the quality of the final motif.
July 2009: GEMS Launcher Release 5.1
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 8.1):
- Includes 132 new matrices (101 fungi (yeast), 27 vertebrate, 2 plant, 1 insect, 1 general core promoter element).
- Library contains now 1106 matrices in 364 families.
- Updated Restriction Site Library (based on REBASE version
907).
- Extended Promoter Module Library (Module
Library Version 5.2):
- CoreSearch:
- Motifs defined from randomly selected subsets can be saved in
"large-scale" CoreSearch version.
- IUPAC conensus sequence of motifs is displayed in "Save Matrices"
table in order to allow easier selection of motifs.
- MatDefine: sequence logos are added for better visualization of matrix consensus sequences
(only available on Genomatix server and GGA).
- GeneRanker: additional annotation type "Signal Transduction Pathways (canonical)" is introduced.
April 2009: GEMS Launcher Release 5.0
-
New Task: GeneRanker, for characterizing sets of genes
- CoreSearch:
- Unlimited number of input sequences (e.g. from ChIP-Seq experiments) are
accepted.
- The new "large-scale" CoreSearch algorithm is used when more than 250 sequences are entered. Definition of a binding motif from about 2000 ChIP-Seq regions usually takes less than 1 minute.
- MatInspector:
- New lines of evidence
to support MatInspector matches:
- Known cocitation (only available on Genomatix server and GGA)
- Known interaction (only available on Genomatix server and GGA)
- Promoter Modules
-
Improved input features
to select promoters from ElDorado/Genomatix Promoter Database to MatInspector.
- Use combo box to select gene of interest
- Map sequence(s) to any organism available in ElDorado
- Interactive result tables that allow sorting and filtering.
December 2008: GEMS Launcher Release 4.8
New features and main changes compared to Release 4.7:
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 8.0):
- Includes 178 new matrices (174 vertebrate, 3 plant, 1 fungi).
- 155 of the new matrices describe homeodomain transcription factor
binding sites.
- 16 of the new vertebrate matrices are derived from ChIP-Chip or
Chip-Seq experiments. These matrices describe binding sites for the
following transcription factors: CMYC, CTCF, ESRRB, GKLF, HNF3B,
HNF4A, NMYC, NRSF, OCT3/4, SOX2, STAT3, TCFCP2L1, USF1, ZFX.
- Library contains now 974 matrices in 325 families.
- Updated Restriction Site Library (based on REBASE version
812).
- Extended Promoter Module Library (Module
Library Version 5.1):
July 2008: GEMS Launcher Release 4.7
New features and main changes compared to Release 4.6.1:
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 7.1):
- Includes 31 new matrices (19 vertebrate, 5 plant, 7 core promoter elements).
- Library contains now 799 matrices in 314 families.
- New matrix group "General Core Promoter Elements"
introduced.
- Matrix group "Others" removed (matrices have been
moved to other groups).
- IUPAC consensus sequence of matrices include also triple-degenerate
IUPAC codes (more information).
- Updated Restriction Site Library (based on REBASE version
806).
- Extended Promoter Module Library (Module
Library Version 5.0):
- Includes 59 new vertebrate modules.
- Library contains now 647 modules (589 vertebrate and 58 plant modules).
- DNA sequences of promoter modules included.
- ModelInspector:
- In case of genome searches, model matches can be exported to BED file format
(only available on the Genomatix server).
January 2008: GEMS Launcher Release 4.6.1
New features and main changes compared to Release 4.6:
- MatInspector:
- New output format of the match table (e.g.
matrix family descriptions are included).
- For single sequence searches, an interactive graphic with the possibility to filter matches is displayed.
- Speed-up of p-value calculations in common TF searches.
November 2007: GEMS Launcher Release 4.6
New features and main changes compared to Release 4.5:
May 2007: GEMS Launcher Release 4.5
New features and main changes compared to Release 4.4:
- The interactive SVG graphics displayed by MatInspector and FrameWorker is
replaced by Genomatix Java Graphics.
- The interactive graphics is implemented as Java applet, running within
your web browser requiring a Java plug-in.
- The Genomatix Java Graphics is faster than the SVG graphics and has
more features (e.g. exporting selected regions of the graphics). For
more details see the graphics
overview.
- FrameWorker:
- The overview graphics now displays a synopsis of the largest frameworks
found, i.e. only TF sites that are part of a framework are shown. The
display can be changed via filter options (to display all common sites,
sites contained in a framework, or sites not contained in a framework)
- In case FrameWorker is started with promoter sequences from Comparative
Genomics in ElDorado or Gene2Promoter,
all annotated promoter
sets can be analysed simultaneously.
- Mandatory elements can be combined with "AND" and
"OR".
- Additional distance constraint parameter "Do restricted model
search". When this parameter is set, more specific models can be
found where the variation of element distances is as small as possible.
- CoreSearch:
- Motifs can occur on both strands (by default, both strands are searched).
- Additional parameter for number of motif matches per sequence: at most
one (default) or any number of repetitions.
- Nucleotide distribution of the input sequences can be taken into account.
This makes sense for motif searches in A/T or G/C rich sequences.
- Previous versions of the matrix and promoter module library
can be selected in order to re-produce old results.
- Per default the latest versions (currently Matrix Library 6.3 and Promoter
Module Library 4.4) are used.
- Matrix Library versions to select in MatInspector and FrameWorker are:
Version 6.1, 6.2, and 6.3.
- Promoter Module Library versions to select in ModelInspector are:
Version 4.2, 4.3, and 4.4.
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 6.3):
- Includes 27 new matrices (21 vertebrate, 6 plant).
- Library contains now 737 matrices in 301 families.
- Updated IUPAC library of plant transcription factor binding
sites
- Based on PLACE Release 30.0.
- Includes 431 TF binding sites in 323 IUPAC families.
- Updated Restriction Site Library (based on REBASE version
704).
- Extended Promoter Module Library (Module
Library Version 4.4):
November 2006: GEMS Launcher Release 4.4
New features and main changes compared to Release 4.3:
- New Project Management: (only
available on the Genomatix server)
- "Result Management" and "Sequence Management"
have been combined into the new "Project Management".
- Grouping of results and sequences into projects possible.
- Comments can be added to projects and results.
- Improved FrameWorker version:
- FrameWorker features an additional distance parameter, the maximum
distance variation between two elements within a model. This allows setting
a higher maximum distance between two elements, but keeping the variation
of distances between the sequences within a certain
"distance band".
- This way, generated frameworks are more likely to be biologically relevant
because the variation in the distance between the elements is set to
an upper limit.
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 6.2):
- Includes 8 new matrices (7 vertebrate, 1 insect).
- Library contains now 713 matrices in 296 families.
- Extended Promoter Module Library (Module
Library Version 4.3):
August 2006: GEMS Launcher Release 4.3
New features and main changes compared to Release 4.2.2:
- New task: Search
for phylogenetically conserved promoter models (only available on
the Genomatix server)
- FastM: Transcription
start site (TSS) added as new element type.
Using the TSS element, it is possible to define transcription factor binding
site models occurring in a specific distance upstream or downstream of the
TSS.
- MatInspector:
- matrix matches below optimized threshold are now colored red in the
output
- all information regarding matrices and families can now be found in MatBase
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 6.1).
- Includes 41 new matrices (33 vertebrate, 5 plant, 3 insect).
- Library contains now 705 matrices in 294 families.
- Updated IUPAC library of plant transcription factor binding
sites
- based on PLACE Release 27.0
- includes 419 TF binding sites in 315 IUPAC families
- Updated Restriction Site Library (based on REBASE version
607).
- Extended Promoter Module Library (Module
Library Version 4.2)
New features and main changes compared to Release 4.2.1:
- FrameWorker: Identification
of promoter frameworks with pre-defined mandatory elements.
- Genomatix Tools: Extended
list comparison with values attached to list elements.
January 2006: GEMS Launcher Release 4.2.1
New features and main changes compared to Release 4.2:
- SNPInspector:
- Allows input of dbSNP identifiers as accession number.
- Thresholds for binding site identification added to input parameters.
- Extended Promoter Module Library (Module
Library Version 4.1)
December 2005: GEMS Launcher Release 4.2
New features and main changes compared to Release 4.1.1:
- New tasks:
- FrameWorker: New
analysis option for alternative promoters
In case the input sequences are Genomatix promoters and alternative promoters
are available for at least one locus, all possible combinations including
one promoter of a locus can be checked automatically. The FrameWorker output
then contains an overview of the frameworks found with each combination of
input sequences as well as a link to the detailed results.
- Transcription start sites annotated in the promoter sequence
file (Genomatix format) are displayed in the alignment.
- ModelInspector:
- In case the Genomatix human, mouse, or rat promoters are scanned with
a model, the search results are evaluated by calculation of z-scores
for groups of the Gene Ontology category "Cellular Component" (in
addition to "Biological Process" and
"Molecular Function").
- Wildcard selection of Promoter Modules from the Module Library possible.
- Sequence Management: Upload of new sequence files to the user's
personal sequence directory possible.
- Download of all results as PDF file possible.
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 6.0).
- Redefinition of all matrices originally based on the TRANSFAC matrix
library. This way we achieved more specific matrices because of a better
alignment of the binding sites and/or removal of weak binding sites.
Furthermore, some erroneous matrices could be corrected.
- Includes 56 new matrices (35 vertebrate, 12 plant, 2 insect, 7 fungi).
- Library contains now 664 matrices in 284 families.
- Updated IUPAC library of plant transcription factor binding
sites
- based on PLACE Release 21.0
- includes 399 TF binding sites in 298 IUPAC families
- Updated Restriction Site Library (based on REBASE version
510).
- Extended Promoter Module Library (Module
Library Version 4.0)
New features and main changes compared to Release 4.1:
- ModelInspector:
- The output contains the genomic location of model matches (e.g. gene
name, promoter, exon, ...) when the Genomatix ElDorado Genomes are scanned
(only available on the Genomatix server).
- Additional parameter that allows to filter the output for sequences
in which a user-specified number of different models have a match.
- Common TF
sites: Common TF sites can be sorted by their p-value in the table
output.
- Extended Promoter Module Library (Module
Library Version 3.8)
- Result Management: Results are sorted alphabetically by task
name.
March 2005: GEMS Launcher Release 4.1
New features and main changes compared to Release 4.0.1:
- New tasks:
- Get primers for a sequence:
Creates primer pairs for one or more sequences according to specifications
like length, melting point, etc.
- Compare (merge/intersect) two lists
- ModelInspector
- Improved Model search threshold: refers to the number of individual
elements of the model and no longer to the sum of the scores of the individual
model elements.
- The output provides ElDorado links
to the genomic location of the matches (if Genomatix promoter databases
or ElDorado genomes are searched).
- In case the Genomatix human, mouse, or rat promoters are scanned with
a model, the search results are evaluated by calculation of z-scores
for groups of the Gene Ontology category "Molecular Function" (in
addition to "Biological Process").
- Comparison of search results with a user-defined list of Locus IDs
possible.
- Common TF
sites:
- A significance value (p-value)
is computed for each common TF site.
- Summary of common TF sites is displayed as table in addition to the
(now optional) graphics output.
- Excel export of summary of common TF sites possible.
- DiAlign TF:
User-defined regions of the alignment can be extracted to a sequence file
which can then be used as input for MatDefine to define a new matrix.
- SNPInspector: Results can
be exported to Excel.
- Switch between "automatic" and "interactive" mode
is possible on each parameter page by clicking the "More options" icon.
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 5.0).
- Includes 42 new matrices (35 vertebrate, 6 plant, 1 other matrices).
- Library contains now 634 matrices in 279 families.
- Additional feature for vertebrate, plant, and insect matrices: percentage
of promoter sequences from ElDorado in which a match to the matrix /
matrix family is found with optimized matrix similarity.
- Updated IUPAC library of plant transcription factor binding
sites
- based on PLACE Release 18.0
- includes 384 TF binding sites in 287 IUPAC families
- Updated Restriction Site Library (based on REBASE version
502).
- Extended Promoter Module Library (Module
Library Version 3.7)
November 2004: GEMS Launcher Release 4.0.1
New features and main changes compared to Release 4.0:
- MatInspector:
Export of statistics and common TFs to Excel format possible.
- Optional input of a name for result files and uploaded sequences.
September 2004: GEMS Launcher Release 4.0
New features and main changes compared to Release 3.8:
- New task DiAlign
TF:
Displays transcription factor binding site matches identified by MatInspector
within the multiple alignment. TF binding site matches can be filtered for
matches that are located in aligned regions.
- FrameWorker:
- Default distance constraints were changed from 10 - 100 bp
to 5 - 50 bp. More than 70 % of the experimentally verified
modules of our Promoter Module Library consist of TF binding sites in
the distance range from 5 to 50 bp, therefore these distance constraints
seem to be suitable to identify functional frameworks.
- Per default only frameworks with a maximum number of 4 elements are
searched as longer frameworks tend to be too specific.
- ModelInspector
- Export of matches to Excel format possible.
- In case the Genomatix human, mouse, or rat promoters are scanned with
a model, the search results are evaluated by calculation of z-scores
for Gene Ontology groups.
- SequenceShaper
- Generated sites are ordered by their matrix similarity.
- Restriction sites either generated or lost by each of the suggested
mutations are shown.
- DiAlign:
additional output parameter "number of nucleic/amino acids per line",
can be set to unlimited so that the complete alignment is shown in one line.
- ExonMapper: alternative mappings
of mRNAs (e.g. splicing variants) are displayed.
- Common TF
sites: the lower limit of sequences which has to contain the common
sites can be defined by the user.
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 4.2).
- Includes 28 new matrices (18 vertebrate, 9 plant, 1 mitochondrial matrices).
- Library contains now 592 matrices in 267 families.
- Plant transcription factors are assigned to the plant matrix families
(389 transcription factors from several plant species).
- Revised IUPAC library of plant transcription factor binding
sites
- based on PLACE Release 16.0
- includes 377 TF binding sites in 285 IUPAC families
- Extended Promoter Module Library (Module
Library Version 3.6)
- Includes 22 new vertebrate modules and
9 new plant modules.
- Library contains now 361 modules (323 vertebrate and 38 plant modules).
- Information whether the vertebrate modules are found also in orthologous
sequences from human, mouse, and rat is included.
- Updated Restriction Site Library
- Based on REBASE version 408.
- Identical restriction sites are merged to one family.
May 2004: GEMS Launcher Release 3.8
New features and main changes compared to Release 3.7:
- FrameWorker: Improved algorithm
resulting in more specific promoter models
- ModelInspector:
New option "only statistics" with unlimited number of matches.
March 2004: GEMS Launcher Release 3.7
New features and main changes compared to Release 3.6:
- New task "SNPInspector:
Identify transcription factor binding sites affected by SNPs (Single Nucleotide
Polymorphisms)"
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 4.1).
- Includes 29 new matrices (10 plant, 17 vertebrate, 1 insect, 1 nematode
matrices).
- Library contains now 564 matrices in 262 families.
- Extended Promoter Module Library (Module
Library Version 3.5)
- Addition of Plant Promoter Modules, library is now divided into the
groups "Vertebrate Modules" and "Plant Modules".
- Includes 36 new vertebrate modules and
28 new plant modules.
- Library contains now 334 modules (305 vertebrate and 29 plant modules).
- MatInspector:
- Extra output added: matches can be displayed aligned with the sequence.
- Nucleotide distribution matrix is shown on matrix help page.
- Matrix family help page lists all promoter modules from the Promoter
Module Library that include the family as an element.
- Matches that occur at the same position on the (+) and (-) strand are
no longer merged. They are both shown in the output to facilitate the
identification of strand-specific common sites.
- Export of matches to Excel format possible.
- FrameWorker:
- Optional determination of a specificity score for the resulting frameworks.
The specificity score is the probability to obtain the frameworks in
a randomly drawn sample of the same size as the input sequence set.
- Common elements are sorted according to their FW-score instead of alphabetically.
This leads to other (better) models if the limit of 100 models is reached.
For all other case, only the order of the models in the output is changed.
- ModelInspector:
- If overlapping matches with the same model score (i.e. matches where
only the location of individual elements differs) are identified, only
one of these matches is shown in the output overview. The other matches
are labeled as "alternative matches" and are shown in the detailed
output.
- Improved performance for very long sequences (> 10 million bp).
December 2003: GEMS Launcher Release 3.6
New features and main changes compared to Release 3.5.3:
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 4.0).
- Includes 50 new matrices (34 plant, 13 vertebrate, 2 insect, 1 fungi
matrices).
- Tissue information added for vertebrate matrices.
- Library contains now 535 matrices in 253 families.
- Revised IUPAC library of plant transcription factor binding
sites
- based on PLACE Release 14.0
- includes 363 TF binding sites in 278 IUPAC families
- Extended Promoter Module Library (Module Library Version 3.4)
- MatInspector:
- Matrices used for the analysis can be filtered by the tissues they
are associated with.
- Matrix family help page lists the transcription factors that are represented
by the family.
- Export of matches to GenBank format (feature table) possible.
- FrameWorker:
- Transcription factors used can be filtered by the tissues they are
associated with.
- Maximum number of elements in the frameworks can be defined by the
user.
- Faster access to sequences entered as database accession numbers.
August 2003: GEMS Launcher Release 3.5.3
Minor changes compared to Release 3.5.2:
- Extended matrix library of transcription factor binding sites
(Matrix Family Library Version 3.3).
- 8 new vertebrate matrices
- 21 new plant matrices
- library contains now 485 matrices in 233 families (describing binding
sites of about 1000 transcription factors)
- Extended Promoter Module Library (Module Library Version 3.3)
Minor changes compared to Release 3.5.1:
- MatInspector 6.2 now allows matrix thresholds like "optimized+0.05"
- Updated information for task "View transcription factor <-> matrix
assignment"
New features and main changes compared to Release 3.5:
- New task "View transcription factor <-> matrix
assignment": allows to check whether a transcription factor is represented
by a Genomatix weight matrix.
- FrameWorker: graphical display
of common elements.
- DiAlign
- Ns in nucleotide sequences are no longer aligned.
- Memory requirements reduced.
March 2003: GEMS Launcher Release 3.5
New features and main changes compared to Release 3.4:
- Completely revised user interface:
- All tasks are available directly from the GEMS
Launcher main menu.
- The tasks are divided in the following groups: Transcription factor
binding sites, Complex regulatory patterns, Alignment, Miscellaneous,
and Genomatix sequence tools.
- New task "Search for common TF sites in multiple sequences" (graphical
display of transcription factor binding sites common to the input sequences).
- FrameWorker can be restarted
using all or selected elements found to be common in all input sequences.
- Protocol function
added: all tasks are logged in the personal protocol file of each user.
- Sequence Management: previously uploaded sequence files can
be edited.
- Revised matrix library of transcription factor binding sites
(Matrix Family Library Version 3.1).
- Extended Promoter Module Library (Module Library Version 3.1)
December 2002: GEMS Launcher Release 3.4
New features and main changes compared to Release 3.3:
- Graphical representation of search results (either as SVG
graphics or as graphics in PNG format) in MatInspector and FrameWorker.
- Sequence input: several sequence files can be selected from
your previously uploaded sequences.
- MatDefine accepts
EMBL and GenBank formatted sequences as input.
- You can search if the transcription factor binding sites you
are interested in are represented by our matrix library.
- New IUPAC library containing plant transcription factor binding
sites:
- based on PLACE Release 11.0
- includes 323 TF binding sites in 258 IUPAC families
- available as task "Search for plant TF sites" in task category "Analyze
your sequences"
- Revised weight matrix library of transcription factor binding
sites (Matrix Family Library Version 3.0)
- Contains 41 new weight matrices (1
bacteria, 40 vertebrate matrices).
- All matrices of a matrix family are now of the same length. This results
in identical positions for the individual matrix matches of a family.
- The library contains now 452 matrices in 216 matrix families.
- Extended Promoter Module Library (Module Library Version 3.0)
May 2002: GEMS Launcher Release 3.3
New features and main changes compared to Release 3.2:
- Local multiple alignment (DiAlign)
- Additional output options:
- several options for meaning of '*' characters below alignment
- user-defined colors for nucleotides and amino acid groups
- Output of pairwise sequence similarities modified.
- ExonMapper
- Improved and faster exon mapping
- Optimized alignment output
- MatInspector:
Sequences of matrix matches can be extracted.
- Result Management: results are now sorted by the GEMS Launcher
task used (instead of program modules as in previous versions).
- Sequence Input: secondary
accession numbers (including secondary accession numbers pointing to several
sequences) are accepted as input.
- Revised weight matrix library of transcription factor binding
sites (Matrix Family Library Version 2.4)
- Contains 32 new weight matrices (1
bacteria, 8 plant, 23 vertebrate matrices).
- Matrix families that do not describe transcription factor binding sites
were moved to a new group called "Other
functional elements".
- The library contains now 412 matrices in 193 matrix families.
- Extended Promoter Module Library (34 new
modules), library contains now 154 modules
November 2001: GEMS Launcher Release 3.2
New features and main changes compared to Release 3.1:
- Revised Category Patterns/Libraries
- Easy access to matrix/model libraries
- Improved conservation profile for matrix help pages
- Model help page access completely revised
- Enhanced result management (added renaming option)
- ExonMapper
- Revised algorithm for mapping exons on antisense strand of a genomic
sequence
- Improved algorithm for long exon mapper runs
- Genomatix sequence tools: added option to extract sequences
in GenBank format (including complete annotation)
- FrameWorker: Graphical output
of framework elements (with option: show all matches)
- ModelInspector:
- Additional output of gene annotation of matches in detailed output
- Identical matches on (+) and (-) strand are merged to a single (+/-)
match
October 2001: GEMS Launcher Release 3.1
New features and main changes compared to Release 3.0:
- Available databases (on Genomatix Server)
- NCBI Reference
Sequences (mRNA sequences) are available as additional database
- EPD and mRNA RefSeq accession
numbers (starting with NM_) can be entered in addition to EMBL/GenBank
accession numbers
- Revised filter options for database searches
- Unlimited number of keywords for restriction of database sequences
- Results from model searches in annotated databases can be filtered
for matches in 3' and 5' UTRS (in addition to exons, introns, repeats,
and promoters)
- DiAlign accepts
also accession numbers as sequence input
- Genomatix sequence tools: extraction of sequences in EMBL
format (including complete annotation) is possible
- Revised weight matrix library of transcription factor binding
sites (Matrix Family Library Version 2.2)
- Contains 20 new weight matrices (2
fungi, 7 insect, 1 plant, 10 vertebrate matrices)
- Revised matrix family classification
- All matrix descriptions are revised, references are available for each
matrix
- Consistent nomenclature of matrix identifiers
April 2001: GEMS Launcher Release 3.0
New features and main changes compared to Release 2.0:
- Sequence Management
- Previously uploaded sequences are stored in the personal directory
for each user
- Sequences can be viewed, deleted, or protected from deletion
- Answers to Frequently Asked Questions (FAQ)
- FrameWorker
- Improved algorithm
- Resulting models can always be saved directly from output
- Additional output options (e.g. sequence of framework elements)
- Pseudographical output of framework positions
- SequenceShaper
- New constraint: conservation of open reading frames possible
- Allows simultaneous deletion of several binding sites
- ExonMapper
- Improved definition of required exon mapping quality
- New database search feature
- Detailed alignment quality report
- Revised alignment and splice site detection
- Local multiple alignment (DiAlign)
- Additional output options (omit nonaligned blocks in output of alignment,
output of pairwise sequence similarities)
- Reduced memory requirements (more or longer sequences can be aligned)
- Enhanced performance
- Model searches (ModelInspector)
- Database search results can be further evaluated by a PubMed search
- Sequences of model matches can be extracted
- Model searches are up to 100 times faster depending on the complexity
of the model and the length of the sequences scanned
- MatInspector
- Subsets of matrices with individually defined core and matrix thresholds
can now be defined
- Revised weight matrix library of transcription factor binding
sites
- based on TRANSFAC 4.4 professional
- contains 27 new weight matrices (5
plant, 22 vertebrate matrices)
- poorly defined weight matrices have been removed
- Extended Promoter Module Library (see list of new
modules)
- Optional modules
- Search for mammalian promoters (PromoterInspector)
- Search for human promoters (requires GPR database) (GPRMapper)
October 2000: GEMS Launcher Release 2.0
New features and main changes compared to Release 1.1:
- New module FrameWorker:
Fully automatic definition of a common framework of transcription
factor binding sites in promoters/enhancers from 2 or more sequences
- New module SequenceShaper:
In silico design of regulatory sequences allowing the generation,
modification and deletion of transcription factor binding sites in DNA
sequences.
- Completely revised ExonMapper:
Fully automatic mapping of cDNA sequences to whole databases
- Enhanced result management
- New filter options for database searches:
- Database searches can be restricted to sequences containing user-defined
keywords
- Results from model searches in annotated databases can be filtered
for matches in exons, introns, repeats or promoters.
- Enhanced algorithm and library for S/MAR location (SMARTest 2.0).
- The revised promoter module library now contains > 100
entries of functionally verified promoter elements.
- Sequence can now also be submitted in plain
text format.
- Transcription factor binding sites:
- Weight matrix library now based on TRANSFAC 4.3 professional.
- TRANSFAC sites are now purged for all sites that would be found by
a matrix also (resulting in non-redundant libraries).
- Easier navigation on help and info pages.
April 2000: GEMS Launcher Release 1.1
New features and main changes compared to Release 1.0:
- New module SMARTest to search
sequences for scaffold / matrix attachment regions.
- Genomatix sequence tools:
little helpers for everyday tasks like reverse-complementing a DNA sequence
or extracting user-defined positions from a sequence.
- First version of result management.
- Enhanced multiple alignment.
- Transcription factor binding sites matches to the same family
from sense and antisense strand are merged by the search routine (less redundant
matches).
- Transcription factor binding site library is based on the
latest TRANSFAC release (4.1).
- Model search results
include statistics for matches in
- exons
- introns
- promoters
- repeats
based on the sequence annotation (only available for sequences in EMBL /
GenBank format).
- Model definition was
changed to allow usage of exact distances between sequence elements.
- Users can define their own model subsets.
- Extended promoter model library (histone promoters modeled
from the EPD).
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